{ "_id": "6a494c8ef6c47c44194996cf", "Package": "npGSEA", "Type": "Package", "Title": "Permutation approximation methods for gene set enrichment\nanalysis (non-permutation GSEA)", "Version": "1.49.0", "Date": "2015-5-6", "Author": "Jessica Larson and Art Owen", "Maintainer": "Jessica Larson ", "Description": "Current gene set enrichment methods rely upon permutations\nfor inference. These approaches are computationally expensive\nand have minimum achievable p-values based on the number of\npermutations, not on the actual observed statistics. We have\nderived three parametric approximations to the permutation\ndistributions of two gene set enrichment test statistics. We\nare able to reduce the computational burden and granularity\nissues of permutation testing with our method, which is\nimplemented in this package. npGSEA calculates gene set\nenrichment statistics and p-values without the computational\ncost of permutations. It is applicable in settings where one\nor many gene sets are of interest. There are also built-in\nplotting functions to help users visualize results.", "License": "Artistic-2.0", "biocViews": "GeneSetEnrichment, Microarray, StatisticalMethod, Pathways", "Collate": "'getIncidence.R' 'miscFunctions.R' 'miscDataPrepFunctions.R'\n'npGSEA.R' 'AllClasses.R' 'AllGenerics.R'\n'npGSEAResultBeta-accessors.R' 'npGSEAResultChiSq-accessors.R'\n'npGSEAResultNorm-accessors.R' 'npGSEAPlot-methods.R'\n'show-methods.R' 'pValues-methods.R'", "Packaged": { "Date": "2026-07-03 19:59:04 UTC", "User": "root" }, "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:01 UTC", "RemoteUrl": "https://github.com/bioc/npGSEA", "RemoteRef": "HEAD", "RemoteSha": "ec632c00f1f4f2f5db5f391ff6f42810e0f20b1c", "NeedsCompilation": "no", "_user": "bioc", "_type": "src", "_file": "npGSEA_1.49.0.tar.gz", "_fileid": "https://r2.ropensci.org/853b2167a53e119dbaab62678924d5e9bd41731781d15aad9dc1385fb37e42c6", "_filesize": 544587, "_sha256": "853b2167a53e119dbaab62678924d5e9bd41731781d15aad9dc1385fb37e42c6", "_expires": "2026-10-12T18:10:20.000Z", "_created": "2026-07-03T19:59:04.000Z", "_published": "2026-07-04T18:10:22.448Z", "_bioccheck": { "error": 1, "warning": 4, "note": 13 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28680767476", "_status": "success", "_upstream": "https://github.com/bioc/npGSEA", "_commit": { "id": "ec632c00f1f4f2f5db5f391ff6f42810e0f20b1c", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379941 }, "_maintainer": { "name": "Jessica Larson", "email": "larson.jess@gmail.com", "login": "lars3313", "description": "Jessica Larson", "uuid": 45085165 }, "_distro": "resolute", "_jobs": [ { "job": 85155089738, "time": 244, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8074048794" }, { "job": 85155089649, "time": 336, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8074065612" }, { "job": 85155089796, "time": 323, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8074063236" }, { "job": 85155089756, "time": 136, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8074028345" }, { "job": 85155089640, "time": 132, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8074027678" }, { "job": 85155089522, "time": 340, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8074000211" }, { "job": 85155089639, "time": 255, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8074050931" }, { "job": 85155089744, "time": 196, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8074040107" }, { "job": 85155089748, "time": 260, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8074051906" }, { "job": 85155089795, "time": 219, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8074044272" } ], "_registered": true, "_dependencies": [ { "package": "GSEABase", "version": ">= 1.24.0", "role": "Depends" }, { "package": "Biobase", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ALL", "role": "Suggests" }, { "package": "genefilter", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "hgu95av2.db", "role": "Suggests" }, { "package": "ReportingTools", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.49.0", "bioc": "3.24" }, { "branch": "release", "version": "1.48.0", "bioc": "3.23" } ], "_topics": [ "genesetenrichment", "microarray", "statisticalmethod", "pathways" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 1, "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/npGSEA.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "alphaValue", "betaHats", "betaStat", "betaValue", "chiSqStat", "DF", "geneSetName", "getIncidence", "npGSEA", "npGSEAPlot", "pLeft", "pRight", "pTwoSided", "pValues", "show", "sigmaSq", "stat", "xSet", "zStat" ], "_help": [ { "page": "alphaValue-methods", "title": "~~ Methods for Function 'alphaValue' ~~", "topics": [ "alphaValue", "alphaValue,npGSEAResultBeta-method", "alphaValue,npGSEAResultBetaCollection-method", "alphaValue-methods" ] }, { "page": "betaHats-methods", "title": "~~ Methods for Function 'betaHats' ~~", "topics": [ "betaHats", "betaHats,npGSEAResultBeta-method", "betaHats,npGSEAResultBetaCollection-method", "betaHats,npGSEAResultChiSq-method", "betaHats,npGSEAResultChiSqCollection-method", "betaHats,npGSEAResultNorm-method", "betaHats,npGSEAResultNormCollection-method", "betaHats-methods" ] }, { "page": "betaStat-methods", "title": "~~ Methods for Function 'betaStat' ~~", "topics": [ "betaStat", "betaStat,npGSEAResultBeta-method", "betaStat,npGSEAResultBetaCollection-method", "betaStat-methods" ] }, { "page": "betaValue-methods", "title": "~~ Methods for Function 'betaValue' ~~", "topics": [ "betaValue", "betaValue,npGSEAResultBeta-method", "betaValue,npGSEAResultBetaCollection-method", "betaValue-methods" ] }, { "page": "chiSqStat-methods", "title": "~~ Methods for Function 'chiSqStat' ~~", "topics": [ "chiSqStat", "chiSqStat,npGSEAResultChiSq-method", "chiSqStat,npGSEAResultChiSqCollection-method", "chiSqStat-methods" ] }, { "page": "DF-methods", "title": "~~ Methods for Function 'DF' ~~", "topics": [ "DF", "DF,npGSEAResultChiSq-method", "DF,npGSEAResultChiSqCollection-method", "DF-methods" ] }, { "page": "geneSetName-methods", "title": "~~ Methods for Function 'geneSetName' ~~", "topics": [ "geneSetName", "geneSetName,npGSEAResultBeta-method", "geneSetName,npGSEAResultBetaCollection-method", "geneSetName,npGSEAResultChiSq-method", "geneSetName,npGSEAResultChiSqCollection-method", "geneSetName,npGSEAResultNorm-method", "geneSetName,npGSEAResultNormCollection-method", "geneSetName-methods" ] }, { "page": "getIncidence", "title": "Determines the incidence of a gene set in a list of genes.", "topics": [ "getIncidence" ] }, { "page": "npGSEA", "title": "Calculates an approximation of the permutation GSEA statistics and p-values", "topics": [ "npGSEA" ] }, { "page": "npGSEAPlot-methods", "title": "~~ Methods for Function 'npGSEAPlot' ~~", "topics": [ "npGSEAPlot", "npGSEAPlot,npGSEAResultBeta-method", "npGSEAPlot,npGSEAResultChiSq-method", "npGSEAPlot,npGSEAResultNorm-method", "npGSEAPlot-methods" ] }, { "page": "npGSEAResultBeta-class", "title": "Class '\"npGSEAResultBeta\"'", "topics": [ "npGSEAResultBeta-class" ] }, { "page": "npGSEAResultBetaCollection-class", "title": "Class '\"npGSEAResultBetaCollection\"'", "topics": [ "npGSEAResultBetaCollection-class" ] }, { "page": "npGSEAResultChiSq-class", "title": "Class '\"npGSEAResultChiSq\"'", "topics": [ "npGSEAResultChiSq-class" ] }, { "page": "npGSEAResultChiSqCollection-class", "title": "Class '\"npGSEAResultChiSqCollection\"'", "topics": [ "npGSEAResultChiSqCollection-class" ] }, { "page": "npGSEAResultNorm-class", "title": "Class '\"npGSEAResultNorm\"'", "topics": [ "npGSEAResultNorm-class" ] }, { "page": "npGSEAResultNormCollection-class", "title": "Class '\"npGSEAResultNormCollection\"'", "topics": [ "npGSEAResultNormCollection-class" ] }, { "page": "pLeft-methods", "title": "~~ Methods for Function 'pLeft' ~~", "topics": [ "pLeft", "pLeft,npGSEAResultBeta-method", "pLeft,npGSEAResultBetaCollection-method", "pLeft,npGSEAResultNorm-method", "pLeft,npGSEAResultNormCollection-method", "pLeft-methods" ] }, { "page": "pRight-methods", "title": "~~ Methods for Function 'pRight' ~~", "topics": [ "pRight", "pRight,npGSEAResultBeta-method", "pRight,npGSEAResultBetaCollection-method", "pRight,npGSEAResultNorm-method", "pRight,npGSEAResultNormCollection-method", "pRight-methods" ] }, { "page": "pTwoSided-methods", "title": "~~ Methods for Function 'pTwoSided' ~~", "topics": [ "pTwoSided", "pTwoSided,npGSEAResultBeta-method", "pTwoSided,npGSEAResultBetaCollection-method", "pTwoSided,npGSEAResultChiSq-method", "pTwoSided,npGSEAResultChiSqCollection-method", "pTwoSided,npGSEAResultNorm-method", "pTwoSided,npGSEAResultNormCollection-method", "pTwoSided-methods" ] }, { "page": "pValues-methods", "title": "~~ Methods for Function 'pValues' ~~", "topics": [ "pValues", "pValues,npGSEAResultBeta-method", "pValues,npGSEAResultChiSq-method", "pValues,npGSEAResultNorm-method", "pValues-methods" ] }, { "page": "sigmaSq-methods", "title": "~~ Methods for Function 'sigmaSq' ~~", "topics": [ "sigmaSq", "sigmaSq,npGSEAResultBeta-method", "sigmaSq,npGSEAResultBetaCollection-method", "sigmaSq,npGSEAResultChiSq-method", "sigmaSq,npGSEAResultChiSqCollection-method", "sigmaSq,npGSEAResultNorm-method", "sigmaSq,npGSEAResultNormCollection-method", "sigmaSq-methods" ] }, { "page": "stat-methods", "title": "~~ Methods for Function 'stat' ~~", "topics": [ "stat", "stat,npGSEAResultBeta-method", "stat,npGSEAResultBetaCollection-method", "stat,npGSEAResultChiSq-method", "stat,npGSEAResultChiSqCollection-method", "stat,npGSEAResultNorm-method", "stat,npGSEAResultNormCollection-method", "stat-methods" ] }, { "page": "show-methods", "title": "~~ Methods for Function 'show' in Package 'base' ~~", "topics": [ "show", "show,npGSEAResultBeta-method", "show,npGSEAResultChiSq-method", "show,npGSEAResultNorm-method", "show-methods" ] }, { "page": "xSet-methods", "title": "~~ Methods for Function 'xSet' ~~", "topics": [ "xSet", "xSet,npGSEAResultBeta-method", "xSet,npGSEAResultBetaCollection-method", "xSet,npGSEAResultChiSq-method", "xSet,npGSEAResultChiSqCollection-method", "xSet,npGSEAResultNorm-method", "xSet,npGSEAResultNormCollection-method", "xSet-methods" ] }, { "page": "zStat-methods", "title": "~~ Methods for Function 'zStat' ~~", "topics": [ "zStat", "zStat,npGSEAResultNorm-method", "zStat,npGSEAResultNormCollection-method", "zStat-methods" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "graph", "GSEABase", "httr", "IRanges", "jsonlite", "KEGGREST", "lifecycle", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "npGSEA.Rnw", "filename": "npGSEA.pdf", "title": "Running gene set enrichment analysis with the \"npGSEA\" package", "engine": "utils::Sweave", "headings": [ "1 Introduction ", "2 Example workflow for GSEA", "3 Methods in brief", "4 Session Info", "5 References" ], "created": "2014-04-04 23:39:58", "modified": "2015-05-06 12:15:06", "commits": 3 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "npgsea", "_universes": [ "bioc", "lars3313" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.49.0", "date": "2026-07-03T20:03:55.000Z", "distro": "resolute", "commit": "ec632c00f1f4f2f5db5f391ff6f42810e0f20b1c", "fileid": "https://r2.ropensci.org/34ecdf76ba873614c91fab76143edd30b319ffb958d3dcdfb532c7bab2b52275", "status": "success", "check": "NOTE", "buildurl": 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